title: 2-Cell Sm strain reverse cross - sample D3

status: Public on May 23 2024

city: København

first: Jason

middle: A

last: Halliwell

address: Blegdamsvej 3B

country: Denmark

institute: The University of Copenhagen

data_processing:
Raw sequencing reads were trimmed, aligned and processed according to Miura et al., 2020 (PMID: 33230331).
Data processing of trimmed abd aligned reads were processed to obtain log2 fold replication timing values according to the methodology described by Miura et al. in their publication from 2020 (PMID: 33230331).
Assembly: mm10
Supplementary files format and content: BedGraph

source_name: 2-Cell Embryo

growth_protocol: To obtain zygotes and 2-cell stage embryos, four to eight-week-old donors were injected with 100µl of 50 I.U. ml-1 (international units) ml−1 solution) solution pregnant mare serum gonadotropin (PMSG) at 17.00 followed by injection of 100µl of 50 I.U. ml-1 human chorionic gonadotropin (hCG) at 17.00 48 hours after PMSG.

extract_protocol:
DNA extraction for single-cell RepliSeq was conducted following established protocols as described in a previous publication (PMID: 33230331).
Library construction was carried out using the protocols established by Miura et al., 2020 (PMID: 33230331), incorporating IDT for Illumina unique dual indexes and the KAPA Hyper Prep Kit from Roche.
single cell RepliSeq

treatment_protocol: In Vitro Ferilized embryos were maintained in KSOM.

value: 2-Cell Embryo

value: 2-cell embryos generated by IVF of CAST/EiJ oocytes and C57/bl6 sperm


title: 2-Cell Sml strain reverse cross - sample C8

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: treatment


title: 2-Cell Sm strain reverse cross - sample D4


title: 2-Cell Sml strain reverse cross - sample C7


title: 26C_48h_1

status: Public on May 24 2024

city: cincinnati

first: XUEZHAO

last: LIU

state: OH

country: USA

institute: cincinnati children's hospital medical center

library_source: transcriptomic

data_processing:
All RNA-seq data were aligned to mm9 or Rn5 using TopHat with default settings (http://tophat.cbcb.umd.edu/). We used Cuff-diff to (i) estimate fragments per kilobase of transcript per million mapped read (FPKM) values for known transcripts and to (ii) analyze differentially expressed transcripts. In all differential expression tests, a difference was considered significant if the p value was less than 0.05.
Assembly: mm10/rn5
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: brain

extract_protocol:
total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: brain

tag: cell line

value: primary iOLs

tag: cell type

value: oligodendrocytes

tag: genotype

value: wildtype


title: 2-Cell Sm strain reverse cross - sample D2


title: 2-Cell Sm strain reverse cross - sample D1


title: neonatal skin fibroblasts, ctr-H2AK119ub

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

country: China

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38
Supplementary files format and content: bigwig

organism: Homo sapiens

source_name: neonatal skin fibroblasts

growth_protocol: BJ fibroblasts were cultured by 10% FBS medium (DMEM, 10%FBS, NEAA, GlutaMAX)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions

treatment_protocol: SS18-SSX1 overexpression by lentiviral infection.

value: skin fibroblasts

value: BJ

value: wild type

tag: chip antibody

value: CST no 8240s

value: EGFP overexpression


title: 2-Cell Sml strain reverse cross - sample C6


title: 2-Cell Sml strain reverse cross - sample C5


title: 2-Cell Sml strain reverse cross - sample C4


title: 2-Cell Sml strain reverse cross - sample C3


title: 2-Cell Sml strain reverse cross - sample C1


title: 2-Cell Sml strain reverse cross - sample C2


title: 2-Cell Se strain reverse cross - sample B3


title: 2-Cell Se strain reverse cross - sample B1


title: 2-Cell G1 strain reverse cross - sample A4


title: 2-Cell G1 strain reverse cross - sample A2


title: 2-Cell G1 strain reverse cross - sample A3


title: 2C Sm NoNoc - Sample C2

data_processing:
*library strategy: single cell RepliSeq
Raw sequencing reads were trimmed, aligned and processed according to Miura et al., 2020 (PMID: 33230331).
Data processing of trimmed abd aligned reads were processed to obtain log2 fold replication timing values according to the methodology described by Miura et al. in their publication from 2020 (PMID: 33230331).
Assembly: mm10
Supplementary files format and content: BedGraph
Supplementary files format and content: bed

extract_protocol:
DNA extraction for single-cell RepliSeq was conducted following established protocols as described in a previous publication (PMID: 33230331).
Library construction was carried out using the protocols established by Miura et al., 2020 (PMID: 33230331), incorporating IDT for Illumina unique dual indexes and the KAPA Hyper Prep Kit from Roche.

value: No Nocodazole synchronization


title: 2C Se NoNoc - Sample B4


title: 2C Se NoNoc - Sample B3


title: 2C Se NoNoc - Sample B2


title: 2C Se NoNoc - Sample B1


title: 2C G1 NoNoc - Sample A2


title: 2C G1 NoNoc - Sample A4


title: 2C Sm NoNoc - Sample C1


title: Zygote G1 post PN - sample A3

source_name: Zygote

value: Zygote

value: Time course from pronuclear formation


title: Zygote G1 post PN - sample A2


title: 2-Cell Se strain reverse cross - sample B2


title: Zygote G1 post PN - sample A1


title: Zygote Hour 8 post PN - sample C4


title: Zygote Hour 7 post PN - sample C3


title: 2-Cell G1 strain reverse cross - sample A1


title: Zygote Hour 7 post PN - sample C2


title: Zygote Hour 8 post PN - sample C5


title: Zygote Hour 7 post PN - sample C1


title: 2C G1 NoNoc - Sample A1


title: Zygote Hour 5 post PN - sample B3


title: Zygote Hour 3 post PN - sample A5


title: Zygote Hour 12 post PN - sample D4


title: WT2

city: Hefei

first: LU

last: Qingshuang

address: 111 Kowloon Road

department: Institute of Physical Science and Information Technology

institute: Anhui University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Main lung  airway section, E13.5

growth_protocol: Pregnant C57 mice with Prmt5 specifically knocked out lung epithelial cells were cultured in a sterile mouse chamber with 60% humidity and 20℃ temperature

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: Lung  airway tissue

value: WT


title: Zygote Hour 5 post PN - sample B1


title: Zygote Hour 5 post PN - sample B2


title: Zygote Hour 12 post PN - sample D2


title: ChIP_YPG_repeat 3

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: paired with ScG3 Input for peak calling

data_processing:
All sequencing protocols were carried out as per the manufacter's instructions using the Illumina NextSeq500 and NextSeq software: base calling was performed using NextSeq Control Software NCS 2.2.0 and Real-time Analysis software RTA 2.4.11 to generate BCL files. The Illumina bcl2fastq2 Conversion Software v2.17 was used to demultiplex sequencing data and convert BCLfiles into FASTQ files.
The quality control and adaptor trimming of sequencing reads were processed by FastQC version 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic version 0.36 with the parameters “2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:3 CROP:68”.
Trimmed reads were mapped to the S. cerevisiae S288C genome using Bowtie2 version 2.3.3.
Bowtie2 mapped BAM files were detected for the ChIP peaks using SPP version 1.13 with a false discovery rate (FDR) of 0.05.
The Sef1 binding peaks were compared and merged among three or four biological replicates by Diffbind version 2.10.0. Only peaks detected in all three biological repeats were used for the downstream analysis.
The text files, wig files, and narrowPeak files were generated from SPP. The bigwig files are generated by deepTools.
Assembly: Saccharomyces cerevisiae S28C genome (R64-2-1)
Supplementary files format and content: Text files with binding positions, wig files, narrowPeak, bigwig files

organism: Saccharomyces cerevisiae

growth_protocol: Cells of W303ScSef1TAPNB1-1 (SEF1-TAP) were grown in the YPD medium at 30°C overnight, subsequently diluted into each indicated medium in a cell density of 0.2 OD600/ml, and then incubated at 30°C for 4.5 h.

extract_protocol:
For breaking cells, 1500 and 500 OD600 of cells from YPD and YPGly, respectively, were thawed and resuspended in FA buffer (50 mM HEPES, pH 7.5; 140 mM NaCl; 0.1% SDS; 1 mM EDTA; 1% Triton X-100; 0.1% Deoxycholate, Na salt) with 1/100 PIC (Protease inhibitor cocktail Set IV, in DMSO; 539136, Merck) and 1 mM phenylmethanesulfonyl fluoride (PMSF, P7626, Sigma) at a concenration of 500 OD600/4ml. Every 4-ml cell suspension was divided into four 2-ml breaking tubes (Biospec, 10832, Microtube 2 ml with cap) containing 1 ml volume of glass beads (11079105, BioSpec Products). The lysis was performed by three cycles of 5-min beating followed by 1-min chilling on ice (Biospec Mini-BeadBeater-16). Cell lysates and glass beads were separated by punching a hole on the bottom of the tube with a red-hot 18G needle and slow centrifugation (500 g, 3 min, 4°C; Eppendorf 5810R centrifuge, A-4-62 rotor). The collected lysates were combined into a 15-ml centrifuge tube and washed with two cycles of 5 ml FA buffer followed by centrifugation (12K rpm, 5 min, 4C; Eppendorf 5810R centrifuge, F-34-6-38 rotor). The washed lysates were completely resuspended in 2 ml FA buffer with 1/100 PIC and 1 mM PMSF in a new 15-ml centrifuge tube (CFT011150, BIOFIL). Chromatin was sheared by sonication in a Bioruptor water bath sonicator (Diagenode) with 15 ml tube-chip unit (High intensity; 30 sec on, 30 sec off, 15 min/cycle; total 3 cycles) at 4°C. The sheared lysate was centrifuged at 12000 g for 10 min at 4°C (Eppendorf 5810R centrifuge, F-34-6-38 rotor). About 25 ml of supernatant corresponding to 5 OD600 of cells was collected, mixed with 200 ml TES buffer (50 mM Tris-Cl, pH 8; 10 mM EDTA, pH 8; 1% SDS) plus 175 ml TE buffer (10 mM Tris-Cl; 1 mM EDTA, pH 8), and stored at -20°C as the input-DNA. Immunoprecipitation was performed by incubating all the rest sheared chromatins with 300 ml Dynabeads® Pan Mouse IgG (11041, human anti-mouse IgG, Invitrogen) in 6 ml of FA buffer with 1/100 PIC and 1 mM PMSF. The binding was performed in a 15-ml tube with mixing using an end-over-end rotator (Fntelli-Mixer, RM-2L, F1 mode, 30 rpm) at 4°C for 16 h. The magnetic beads were anchored with DynaMagTM-2 Magnet and the bound complexes were washed 4 times with 1 ml of each wash buffer for 5 min [FA buffer × 1, high-salt FA buffer (50 mM HEPES, pH 7.5; 500 mM NaCl; 0.1% SDS; 1 mM EDTA; 1% Triton X-100; 0.1% Deoxycholate, Na salt) × 1, DOC buffer (10 mM Tris·Cl; 1 mM EDTA, pH 8; 25 0mM LiCl; 0.5% IGEPAL® CA-630; 0.5% Deoxycholate, Na salt) × 1, and TE buffer × 1] with mixing (Fntelli-Mixer, RM-2L, F1 mode, 30 rpm) at room temperature. The bound complexes were eluted twice by heating at 65°C in 200 ml TES buffer for 20 min and in 200 ml TE buffer for 10 min. Two eluates were pooled as the ChIP-DNA. To remove RNA, both the input-DNA and ChIP-DNA (~400 ml each) were treated with 5 ml of 10 mg/ml RNase A (R5503, Sigma; 100 mM Tris-Cl, pH 7.4) at 37°C for 30 min. For de-crosslinking, both the RNase-treated input-DNA and ChIP-DNA were treated with 40 ml of 20 mg/ml Proteinase K (1.24568.0500, Merck; in 50 mM Tris-Cl, pH 8) at 42°C for 1 h and then 65°C for 16 h. De-crosslinked DNA was purified using the QIAquick DNA Purification Kit (28106, Qiagen) according to the manufacturer's instruction, with a modification of a two-cycle wash step using the PE buffer. Final ChIP-DNA and input-DNA were eluted with 50 ml EB buffer. DNA concentrations were measured by using the Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen by Thermo Fisher Scientific).
ChIP-seq analysis was performed from three biological replicates of YPD- and YPGly-grown cells. The average fragment length of sonicated fragments was 150–1000 bp. For each condition, libraries were prepared from >3 ng of ChIP-DNA and input-DNA using the KAPA LTP Library Preparation Kit for Illumina® platforms (KK8232, KAPA Biosystems by Roche) according to the manufacturer’s instruction. Notably, after adapter ligation, double-sided size selection between 250–450bp for adapter-ligated fragments was performed using the KAPA Pure Beads (KK8000/07983271001, KAPA Biosystems by Roche). Size-selected fragments were then PCR-amplified for 12 cycles. The size of each library was assessed using a Bioanalyzer 2100 instrument (Agilent Technologies) with the High Sensitivity DNA Kit (Agilent Technologies). The concentration of each library was quantified by using the Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen by Thermo Fisher Scientific) and qPCR. Single-read sequencing (75 bp) or paired-end sequencing (75 bp × 2) of the libraries was performed using the NextSeq 500/550 high output reagent kit V2_75 cycle (FC-404-2005, Illumina) on an Illumina NextSeq500 sequencer.

treatment_protocol: After 4.5 h of incubation at 30°C, cultures of log phase cells (1 OD600/ml in YPD and 0.4 OD600/ml in YPGly) were fixed with 1% formaldehyde at 25°C for 15 min with shaking at 180 rpm and then quenched with 125 mM glycine at 25°C for 10 min with shaking at 180 rpm. All the following steps were performed in an ice-cold or 4°C environment. Cells were harvested, washed twice with TBS (20 mM Tris-Cl, pH 7.5; 150 mM NaCl), and stored at −80°C until use.

tag: strain

tag: condition

value: YPGly, 30°C

tag: time

tag: growth phase

value: log-phase, OD = ~0.4


title: ChIP_YPD_repeat 4

description: paired with ScD4 Input for peak calling

value: YPD, 30°C

value: log-phase, OD = ~1.0


title: Input_YPGly_repeat 1

description: paired with ScG1 ChIP for peak calling


title: ChIP_YPGly_repeat 2

description: paired with ScG2 ChIP for peak calling


title: MU2

value: Prmt5 knockdown


title: WT1


title: Zygote Hour 6 post PN - sample B5


title: 2C G1 NoNoc - Sample A3

value: 2-Cell Embryo


title: ChIP_YPGly_repeat 3

description: paired with ScG3 ChIP for peak calling


title: ChIP_YPD_repeat 2

description: paired with ScD2 Input for peak calling


title: MU1


title: WT3


title: ChIP_YPD_repeat 1

description: paired with ScD1 Input for peak calling


title: Zygote Hour 12 post PN - sample D3


title: Input_YPD_repeat 3

description: paired with ScD3 ChIP for peak calling


title: ChIP_YPD_repeat 3

description: paired with ScD3 Input for peak calling


title: ChIP_YPG_repeat 1

description: paired with ScG1 Input for peak calling


title: ChIP_YPG_repeat 2

description: paired with ScG2 Input for peak calling


title: Input_YPD_repeat 2

description: paired with ScD2 ChIP for peak calling


title: Input_YPD_repeat 1

description: paired with ScD1 ChIP for peak calling


title: SKOV3 cells, Daphnetin(40mg/L) 1

city: Chang chun

first: Ning

last: Ma

address: Xinmin Road 71, The First Hospital of Jilin University

institute: The First Hospital of Jilin University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ovarian tissue

growth_protocol: A2780 and SKOV3 cells were cultured in DMEM (10% FBS and 1% penicillin/streptomycin) and RPMI-1640 (15% FBS and 1% penicillin/streptomycin)

extract_protocol:
2 μg total RNAs were used for the constructlon of sequencing libraries.
RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina®  following the manufacturer’s instruction.

value: ovarian tissue

value: ovarian cancer cell


title: SKOV3 cells, Daphnetin(40mg/L) 3


title: SKOV3 cells, Daphnetin(40mg/L) 2


title: SKOV3 cells, Daphnetin(20mg/L) 2


title: SKOV3 cells, Daphnetin(20mg/L) 3


title: SKOV3 cells, Daphnetin(20mg/L) 1


title: A2780 cells, Daphnetin(40mg/L) 3


title: SKOV3 cells, DMSO 1

value: DMSO


title: SKOV3 cells, DMSO 2


title: SKOV3 cells, DMSO 3


title: A2780 cells, Daphnetin(20mg/L) 3


title: A2780 cells, Daphnetin(40mg/L) 2


title: A2780 cells, DMSO 3


title: Th17_72h_H3K27me3_rep1

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly with Bowtie2
Reads with quality value < 30 were filtered out using samtools and duplicate reads were removed using Picard tools' MarkDuplicates function
Bigwig files were generated using deeptools' bamCoverage function with the following settings: --binsize 10 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --ignoreForNormalization chrX
During bigwig file generation reads were extended based on the fragment length of each sample
Assembly: hg38
Supplementary files format and content: bigWig

source_name: blood

growth_protocol: CD4+ T cells were isolated from human umbilical cord blood using magnetic bead based positive selection

extract_protocol:
Fragmented genomic DNA (input) or after pull down with respective histone antibody was used for library preparation.
Illumina Truseq

treatment_protocol: CD4+ T cells from multiple donors (three or more) were  pooled before activation with plate-bound anti-CD3 (3750 ng/6-well culture plate well) (Beckman Coulter, cat# IM-1304) and soluble anti-CD28 (1 μg/mL) (Beckman Coulter, cat# IM1376) at the density of 0.5 × 106 cells/mL of X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) supplemented with L-glutamine (2 mM, Sigma-Aldrich, Dorse, UK) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich). Th17 cell polarization was initiated with a cytokine cocktail of IL6 (20 ng/mL; Roche, cat# 11138600 001), IL1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) in the presence of neutralizing anti-IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and anti-IL4 (1 μg/mL, R&D Systems, cat# MAB204).

value: blood

value: CD4+ T cells

value: Cells activated with CD3 CD28 in presence of Th17 polarising cytokines (IL-6, IL-1Beta, TGF-Beta) and neutralizing antibody against IL-4 and IFNgamma

tag: time point

value: 72 hours

tag: antibody


title: Th17_72h_H3K4me1_rep3


title: A2780 cells, Daphnetin(40mg/L) 1


title: A2780 cells, DMSO 2


title: Th17_72h_H3K27ac_rep3


title: Input_YPD_repeat 4

description: paired with ScD4 ChIP for peak calling


title: A2780 cells, DMSO 1


title: Th17_72h_Input_rep3

value: Input


title: Th17_72h_H3K4me3_rep3


title: Th0_72h_H3K27me3_rep1

value: Cells activated with CD3 CD28 in absense of cytokines


title: Th0_72h_H3K27ac_rep3


title: Th0_72h_H3K4me1_rep3


title: Th0_72h_Input_rep3


title: Th17_0.5h_H3K27ac_rep3

value: 0.5 hours


title: A2780 cells, Daphnetin(20mg/L) 1

value: WT


title: A2780 cells, Daphnetin(20mg/L) 2


title: Th0_0.5h_H3K4me3_rep3


title: Th0_0.5h_H3K4me1_rep3


title: Th17_0.5h_H3K4me1_rep3


title: Th17_0.5h_H3K4me3_rep3


title: Th0_0.5h_H3K27ac_rep3


title: Th17_72h_H3K4me1_rep2


title: Th0_72h_H3K4me3_rep3


title: Th17_72h_Input_rep2


title: Th0_72h_H3K4me3_rep2


title: Th0_72h_H3K27ac_rep2


title: Th0_0.5h_Input_rep3


title: Th0_72h_Input_rep2


title: MCF7_OC2oe_3

city: Pamplona

first: Mirja

last: Rotinen

state: Navarre

address: Avenida Barañain s/n

department: Health Sciences

country: Spain

institute: Public University of Navarre

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.7.0d with default parameters.
featureCounts v1.6.0 software and Gencode v38 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

molecule: polyA RNA

growth_protocol: MCF-7 cells were grown in RPMI-1640 media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen). 300 ng of total RNA was used for the construction of sequencing libraries
RNA was subjected to quantity and quality control using Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity RNA ScreenTape (Agilent Technologies). All RNA samples were high-quality, with RIN values higher than 7. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Lentivirus were created by cotransfection of the pCMV-Delta-8.2 packaging plasmid, the pCMV-VSVG plasmid and the OC2 overexpression or empty plasmid (Origene) into HEK-293 cells. MCF-7 cells were subsequently transduced and selected on puromycin to create the stable lines.

tag: transfection

value: OC2 overexpression


title: Th17_0.5h_H3K27ac_rep2


title: Th17_72h_H3K4me3_rep2


title: Th17_72h_H3K27ac_rep2


title: Th17_0.5h_Input_rep2


title: Th17_0.5h_H3K4me1_rep2


title: Th0_72h_H3K4me1_rep2


title: Th17_0.5h_H3K4me3_rep2


title: MCF7_OC2oe_1


title: MCF7_OC2oe_2


title: Th0_0.5h_H3K4me3_rep2


title: MCF7_C_2

value: empty


title: Th0_0.5h_H3K27ac_rep2


title: MCF7_C_3


title: MCF7_C_1


title: Th17_0.5h_Input_rep3


title: Th0_0.5h_H3K4me1_rep2


title: BT474_OE_3

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR 2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode v42 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

growth_protocol: BT-474 cells were grown in RPMI-1640 media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen). 300 ng of total RNA was used for the construction of sequencing libraries
RNA was subjected to quantity and quality control using Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity RNA ScreenTape (Agilent Technologies). All RNA samples were high-quality, with RIN values higher than 7. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly,the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Lentivirus were created by cotransfection of the pCMV-Delta-8.2 packaging plasmid, the pCMV-VSVG plasmid and the OC2 overexpression or empty plasmid (Origene) into HEK-293 cells. BT-474 cells were subsequently transduced and selected on puromycin to create the stable lines.


title: Th0_0.5h_Input_rep2


title: BT474_OE_1


title: Th17_72h_H3K27ac_rep1


title: BT474_OE_2


title: Bur-0_W+N+_P3ID34_c

city: Versailles

first: Olivier

last: Loudet

address: Rte de St Cyr

department: IJPB

country: France

institute: INRAE

data_processing:
Adapter sequences and bases with a Q-Score below 20 were trimmed out from reads using Trimmomatic (v0.36, Bolger et al. 2014) and reads shorter than 30 bases after trimming were discarded. Reads corresponding to rRNA sequences were removed using sortMeRNA (v2.1, Kopylova E. et al. 2012) against the silva-bac-16s-id90, silva-bac-23s-id98, silva-euk-18s-id95 and silva-euk-28s-id98 databases.
The pipeline combined with hisat2 and feature count was used to align reads against the Arabidopsis thaliana transcriptome Araport11 (Cheng et al., 2017).
The abundance of each gene was calculated by a feature count using the default function.
The percentages of the reads that are successfully mapped to only a single genomic location of the Col-0 genome ranged from 82.19% to 91.92% among accessions. All samples were sequenced and processed following the same process.
Assembly: Araport11
Supplementary files format and content: A text file is submitted with raw gene counts for every gene in every sample

organism: Arabidopsis thaliana

source_name: Arabidopsis rosette

growth_protocol: Seeds were treated with 0.1% agarose and stratified at 4°C in darkness for three days before sowing. Seeds were then sown on unfertilised peat moss soil plugs and transferred to a short-day culture chamber (8 hours photoperiod at 230 μmol.m−2.s−1 light, with days at 21 °C/65%RH and nights at 17 °C/65% RH), where -after 8 days- they were installed on a Phenoscope robot (https://phenoscope.versailles.inra.fr/) for 23 days' culture under 4 different growth conditions. Sampled rosettes have 31 days after sowing.

extract_protocol:
total RNAs were isolated from the RNeasy Plant Mini kit (Qiagen) following the manufacturer’s recommendations.
RNA-seq libraries were constructed by the POPS platform (IPS2) using the TruSeq Stranded mRNA library prep kit (Illumina®, California, U.S.A.) according to the supplier’s instructions.

treatment_protocol: We use Phenoscope, a high throughput phenotyping robot to apply treatment during the vegetative stage (Tisné et al., 2013). We applied a combination of soil water content (SWC; adjusted with respect to complete soil saturation) and nutrient solution (adjusted to provide a specific amount of nitrate over the course of the experiment : 160.45 ± 7.96 ml of 5mM [Nitrate] nutrient solution in total for the control condition W+N+; 50.85 ± 4.67 ml of 5mM [Nitrate] in total for the single drought stress condition W-N+; 161.93 ± 11.07 ml of 0.5mM [Nitrate] in total for the single N-deficiency condition W+N-; 50.70 ± 4.10 ml of 1.5mM [Nitrate] in total for the combined stress condition W-N-) to establish the different conditions.

value: leaf

value: W+N+


title: Bur-0_W+N+_P3ID34_a


title: Tsu-0_W-N-_P3ID34_d

value: W-N-


title: Tsu-0_W-N-_P3ID33_e


title: Th17_72h_H3K4me3_rep1


title: BT474_C_2


title: Tsu-0_W-N-_P3ID33_c


title: Th17_72h_H3K4me1_rep1


title: Th17_72h_Input_rep1


title: Th0_72h_H3K27ac_rep1


title: Tsu-0_W-N-_P3ID34_b


title: BT474_C_1


title: 1_20_1_1_Group_3_Non_lame

city: Midlothian

first: SEUNGMEE

last: LEE

address: Easter Bush Campus

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

description: Male (gelding)

library_source: other

data_processing:
Raw sequence data converted to fastq files and de-multiplexed using the bcl2fastq software (Illumina inc)
Trimming for adapters was performed using Cutadapt v1.11
Mapping was performed using Mapping Bowtie2 (v 2.2.2)
Assembly: EquCab2, annotation reference: mirbase_20
Supplementary files format and content: miRNA raw_counts: comma separated values containing raw reads, and miRNA names with associated sequence for each sample

molecule: other

organism: Equus caballus

source_name: plasma

extract_protocol:
Plasma was isolated from EDTA treated whole blood by centrifugation at 1100g for 10 mins within 4 hours of collection. RNA was isolated using the miRNeasy Serum/Plasma Kit (Cat. 217184, Qiagen) according to manufacturer’s instructions.
The libraries were generated using the QIAseq miRNA Library Kit (Cat.331502, Qiagen).

value: plasma


title: Col-0_W-N+_P3ID34_c

value: W-N+


title: Th0_72h_H3K4me3_rep1


title: Tsu-0_W+N-_P3ID33_f

value: W+N-


title: Tsu-0_W+N-_P3ID34_d


title: 1_9_1_1_Group_2_Non_fracture_lame

description: Male (gelding)


title: Tsu-0_W+N-_P3ID33_e


title: Tsu-0_W+N-_P3ID33_c


title: Th0_72h_H3K4me1_rep1


title: Tsu-0_W+N-_P3ID34_b


title: 1_7_1_1_Group_2_Non_fracture_lame

description: Male (gelding)


title: Tsu-0_W+N-_P3ID34_a


title: Tsu-0_W-N+_P3ID33_f


title: Th0_72h_Input_rep1


title: Th17_0.5h_H3K27ac_rep1


title: Tsu-0_W-N-_P3ID33_f


title: BT474_C_3


title: Tsu-0_W-N+_P3ID33_e


title: Th17_0.5h_H3K4me3_rep1


title: 1_16_1_1_Group_3_Non_lame

description: Male (gelding)


title: Tsu-0_W-N-_P3ID34_a


title: 1_5_1_1_Group_1_Stress_fracture

description: Female (mare)


title: Tsu-0_W-N+_P3ID34_b


title: Th17_0.5h_H3K4me1_rep1


title: 1_8_1_1_Group_2_Non_fracture_lame

description: Male (gelding)


title: Th17_0.5h_Input_rep1


title: Col-0_W-N+_P3ID34_b


title: Tsu-0_W-N+_P3ID34_c


title: 1_17_1_1_Group_3_Non_lame

description: Male (gelding)


title: Th0_0.5h_H3K27ac_rep1


title: Tsu-0_W+N+_P3ID33_f


title: Tsu-0_W+N+_P3ID33_d


title: Tsu-0_W+N+_P3ID33_e


title: 1_3_1_1_Group_2_Non_fracture_lame

description: Male (gelding)


title: Tsu-0_W+N+_P3ID34_c


title: Th0_0.5h_H3K4me3_rep1


title: 1_13_1_1_Group_1_Stress_fracture

description: Male (gelding)


title: Tsu-0_W+N+_P3ID34_b


title: Th0_0.5h_H3K4me1_rep1


title: Tsu-0_W+N+_P3ID34_a


title: Sha_W-N-_P3ID33_f

value: Sha


title: 1_10_1_1_Group_1_Stress_fracture

description: Male (gelding)


title: Sha_W-N-_P3ID33_e


title: Th0_0.5h_Input_rep1

value: blood


title: Tsu-0_W-N+_P3ID33_d


title: 1_6_1_1_Group_1_Stress_fracture

description: Male (gelding)


title: Sha_W-N-_P3ID33_d


title: 1_18_1_1_Group_3_Non_lame

description: Male (gelding)


title: Col-0_W-N+_P3ID33_a


title: 1_19_1_1_Group_3_Non_lame

description: Male (gelding)


title: D2_Th17_72h

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly with Bowtie2
Reads mapping to ChrM and reads with mapping quality value < 30 were filtered out using samtools and duplicate reads were removed using Picard tool's MarkDuplicates function.
Peaks were called using MACS2 with the following settings: -g hs -q 0.05
Assembly: hg38
Supplementary files format and content: narrowPeak files were generated with MACS2

source_name: cord blood

extract_protocol:
The nucleii were exptracted as described in Henricksson et al 2019 (https://doi.org/10.1016/j.cell.2018.11.044)
The libraries were prepared as described in Henricksson et al 2019 (https://doi.org/10.1016/j.cell.2018.11.044)

treatment_protocol: CD4+ T cells from two donors (D1 and D2) were activated with plate-bound anti-CD3 (3750 ng/6-well culture plate well) (Beckman Coulter, cat# IM-1304) and soluble anti-CD28 (1 μg/mL) (Beckman Coulter, cat# IM1376) at the density of 0.5 × 106 cells/mL of X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) supplemented with L-glutamine (2 mM, Sigma-Aldrich, Dorse, UK) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich). Th17 cell polarization was initiated with a cytokine cocktail of IL6 (20 ng/mL; Roche, cat# 11138600 001), IL1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) in the presence of neutralizing anti-IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and anti-IL4 (1 μg/mL, R&D Systems, cat# MAB204).

value: cord blood

value: CD4+ T cells


title: Tsu-0_W-N+_P3ID34_a


title: Sha_W-N-_P3ID34_a


title: 1_1_1_1_Group_1_Stress_fracture

description: Male (gelding)


title: D1_Th17_72h

value: Cells activated with CD3 CD28 in presence of Th17 polarising cytokines (IL-6, IL-1Beta, TGF-Beta) and neutralizing antibody against IL-4 and IFNgamma

value: 72 hours


title: Sha_W+N-_P3ID33_f


title: Sha_W+N-_P3ID33_e


title: D2_Th17_48h

value: 48 hours


title: 1_2_1_1_Group_2_Non_fracture_lame

description: Female (mare)


title: D1_Th17_48h


title: Sha_W+N-_P3ID34_c


title: Sha_W+N-_P3ID33_b


title: Sha_W+N-_P3ID34_a


title: D2_Th17_24h

value: 24 hours


title: lpwRCC594, LP-WGS

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end sequencing reads were trimmed and aligned to the hg19 human reference genome using Burrows–Wheeler Aligner version 0.7.1740.
Non-uniquely mapping and duplicate reads were discarded. Peak calling was performed using MACS version 2.1.1.2014061641 with a q value (false discovery rate (FDR)) threshold of 0.01.
Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Fragment locations were inferred from mapped read pairs in BAM files and converted to BED format using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set.
bigWig files were generated using the genomicRanges R package.
circulating tumor DNA fraction in plasma samples was estimating using LP-WGS with ichorCNA.
Assembly: hg19
Supplementary files format and content: BigWig, narrowPeak (except for Input)
Library strategy: LP-WGS

source_name: Plasma

extract_protocol:
Tissue was fixed by 2mmol/L disuccinimidyl glutarate (DSG) for 10 minutes followed by 1% formaldehyde for 10 minutes, and quenched with glycine. Chromatin was sheared using the Covaris E220Ultrasonicator.
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio. Libraries were sequenced using 150-base paired-end reads on an Illuminaplatform.

value: Plasma

tag: histology

value: Sarcomatoid

value: LP-WGS


title: Sha_W-N+_P3ID33_f

value: leaf


title: Col-0_W+N+_P3ID33_f

value: W+N+


title: lpwRCC2975, LP-WGS

value: Epitehlioid


title: Sha_W-N+_P3ID33_e


title: Sha_W-N+_P3ID34_d


title: D2_Th17_4h

value: WT

value: 4 hours


title: Sha_W-N-_P3ID34_b

value: W-N-


title: Sha_W-N+_P3ID33_c

value: Sha

value: W-N+


title: Sha_W-N-_P3ID34_c


title: lpwRCC2974, LP-WGS


title: D1_Th17_4h

value: cord blood


title: Sha_W-N+_P3ID34_a


title: D2_Th17_2h

value: CD4+ T cells

value: 2 hours


title: lpwRCC2973, LP-WGS


title: lpwRCC2971, LP-WGS


title: Sha_W+N+_P3ID34_d


title: Sha_W+N+_P3ID33_e


title: Sha_W+N-_P3ID34_d

value: W+N-


title: Sha_W+N+_P3ID33_c


title: D2_Th0_72h

value: Cells activated with CD3 CD28 in absense of cytokines

value: 72 hours


title: lpwRCC2970, LP-WGS

value: Plasma


title: lpwRCC478, LP-WGS

value: Sarcomatoid


title: D1_Th17_24h

value: Cells activated with CD3 CD28 in presence of Th17 polarising cytokines (IL-6, IL-1Beta, TGF-Beta) and neutralizing antibody against IL-4 and IFNgamma

value: 24 hours


title: Sha_W+N+_P3ID34_b

value: leaf

value: W+N+


title: Col-0_W+N+_P3ID34_e


title: D1_Th0_72h

value: WT


title: lpwRCC2194, LP-WGS

value: LP-WGS


title: lpwRCC2031, LP-WGS


title: Cvi-0_W-N-_P3ID33_f

value: W-N-


title: D2_Th0_48h

value: 48 hours


title: Sha_W+N+_P3ID34_a

value: Sha


title: Sha_W-N+_P3ID34_b

value: W-N+


title: Cvi-0_W-N-_P3ID33_c


title: Cvi-0_W-N-_P3ID34_e


title: D1_Th0_48h

value: cord blood

value: CD4+ T cells


title: lpwRCC1764, LP-WGS


title: Sha_W+N+_P3ID33_f


title: mdRCC594, MeDIP, MeDIP-seq

data_processing:
Paired-end sequencing reads were trimmed and aligned to the hg19 human reference genome using Burrows–Wheeler Aligner version 0.7.1740.
Non-uniquely mapping and duplicate reads were discarded. Peak calling was performed using MACS version 2.1.1.2014061641 with a q value (false discovery rate (FDR)) threshold of 0.01.
Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Fragment locations were inferred from mapped read pairs in BAM files and converted to BED format using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set.
bigWig files were generated using the genomicRanges R package.
circulating tumor DNA fraction in plasma samples was estimating using LP-WGS with ichorCNA.
Assembly: hg19
Supplementary files format and content: BigWig, narrowPeak (except for Input)

value: MeDIP


title: D2_Th0_24h

value: Cells activated with CD3 CD28 in absense of cytokines


title: Cvi-0_W-N-_P3ID34_a


title: D1_Th17_2h

value: 2 hours


title: mdRCC478, MeDIP, MeDIP-seq

value: Plasma


title: Cvi-0_W+N-_P3ID34_e

value: W+N-


title: Cvi-0_W+N-_P3ID33_d


title: D1_Th0_24h


title: D2_Th0_4h

value: 4 hours


title: mdRCC2975, MeDIP, MeDIP-seq

value: Epitehlioid


title: Col-0_W+N+_P3ID33_d

value: leaf


title: Cvi-0_W+N-_P3ID34_c


title: mdRCC2974, MeDIP, MeDIP-seq


title: Cvi-0_W-N-_P3ID33_d


title: D1_Th0_4h


title: Cvi-0_W+N-_P3ID33_b


title: Cvi-0_W+N-_P3ID34_a


title: Cvi-0_W-N+_P3ID34_f


title: D2_Th0_2h


title: mdRCC2973, MeDIP, MeDIP-seq


title: Cvi-0_W-N-_P3ID34_b


title: D1_Th0_2h


title: mdRCC2971, MeDIP, MeDIP-seq


title: Cvi-0_W-N+_P3ID34_d


title: D2_Thp

value: untreated


title: Cvi-0_W-N+_P3ID33_c


title: Cvi-0_W-N+_P3ID34_b


title: Cvi-0_W-N+_P3ID33_a


title: mdRCC2970, MeDIP, MeDIP-seq


title: mdRCC2194, MeDIP, MeDIP-seq

value: Sarcomatoid


title: Cvi-0_W+N-_P3ID33_f


title: D1_Thp

value: WT


title: Cvi-0_W+N+_P3ID33_f

value: W+N+


title: Cvi-0_W+N+_P3ID34_e


title: mdRCC1764, MeDIP, MeDIP-seq


title: mdRCC2031, MeDIP, MeDIP-seq


title: Cvi-0_W+N+_P3ID33_d


title: K4_RCC594, H3K4me3, ChIP-seq


title: Cvi-0_W+N+_P3ID33_b


title: Cvi-0_W-N+_P3ID33_e


title: K4_RCC478, H3K4me3, ChIP-seq


title: Cvi-0_W+N+_P3ID34_a


title: 3d PA CD44loSca1+ _ 3

city: Chicago

first: Qian

last: Chen

state: IL

address: 909 S Wolcott avenue, COMRB 4160

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Illumina CASAVA was used for base calling
Adapters were trimmed from sequence, and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the reference genome using STAR (Dobin et al, 2013).
Read counts for each gene were calculated using htseq-count (Anders et al, 2015)
Normalization and differntial expression were determined using DESeq2 (Love et al, 2014). Differential expressed genes with FDR-adjusted p-value less than 0.05 were determined significant.
Assembly: mm10
Supplementary files format and content: A DESeq2 output containing normalized abundance measurements for each sample

source_name: Lung

extract_protocol:
AT2 cells FACS sorted from lineage traced mice. Total RNA was extracted using the RNAqueous-Micro Total RNA isolation kit (ThermoFisher). TruSeq mRNA-Seq libraries was prepared and sequenced on the Illumina Hiseq 4000 platform with production of single-end, 50 bp reads.
The Illiumina Stranded mRNA-Seq library Preparation Kit was used to prepare sequencing libraries

value: Lung

value: 3d PA


title: 3d PA CD44loSca1- _3


title: Cvi-0_W+N+_P3ID34_c


title: Col-0_W-N-_P3ID34_e

value: W-N-


title: K4_RCC2975, H3K4me3, ChIP-seq


title: Col-0_W-N-_P3ID33_f


title: 3d PA CD44loSca1+ _ 2


title: Col-0_W-N-_P3ID33_c


title: K4_RCC2974, H3K4me3, ChIP-seq


title: Col-0_W-N-_P3ID34_b


title: Col-0_W-N-_P3ID34_d


title: 3d PA CD44loSca1- _2


title: Col-0_W+N+_P3ID33_b


title: 3d PA CD44hi _1


title: 3d PA CD44hi _3


title: Col-0_W+N-_P3ID34_f


title: Col-0_W+N+_P3ID34_c


title: Col-0_W+N-_P3ID33_e


title: K4_RCC2971, H3K4me3, ChIP-seq


title: Col-0_W+N-_P3ID34_d


title: Col-0_W+N-_P3ID33_a


title: 3d PA CD44hi _2


title: 3d PA CD44loSca1- _1


title: K4_RCC2194, H3K4me3, ChIP-seq


title: Col-0_W+N-_P3ID34_b


title: Col-0_W+N-_P3ID33_c


title: K4_RCC2031, H3K4me3, ChIP-seq


title: K4_RCC2970, H3K4me3, ChIP-seq


title: nonPA CD44hi_2

description: SB

value: Untreated


title: K4_RCC1764, H3K4me3, ChIP-seq


title: nonPA CD44hi_1

description: SA


title: Bur-0_W-N-_P3ID34_d


title: Col-0_W-N-_P3ID33_a


title: Col-0_W-N+_P3ID34_f

value: W-N+


title: Bur-0_W-N-_P3ID33_e


title: Bur-0_W-N-_P3ID33_f


title: Astrocyte day60 rep2

city: Beijing

first: Song

last: Wang

address: NO.95, Yong'An Road, Xicheng District

institute: Beijing Friendship Hospital, Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.3.4.2
The read numbers of the corresponding genes were counted via HTSeq v0.6.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw conuts for each Sample

source_name: cerebral cortex

extract_protocol:
Astrocytes were isolated via FACS, and RNA was harvested using Qiagen RNeasy MinElute Cleanup Kit (Cat NO. 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The distal middle cerebral artery (MCA) was permanently ligated with 10-0 sutures followed by 7 min of occlusion of the bilateral common carotid artery (CCA). The sham control group only received skull surface lesions.

value: cerebral cortex

value: Astrocyte

value: WT C57BL/6J

value: ischemic stroke


title: Astrocyte day60 rep1


title: Bur-0_W-N-_P3ID34_b


title: Bur-0_W-N-_P3ID33_c


title: Bur-0_W-N-_P3ID34_a


title: K27_RCC594, H3K27, ChIP-seq

value: Plasma


title: 3d PA CD44loSca1+ _ 1


title: K27_RCC478, H3K27, ChIP-seq


title: K4_RCC2973, H3K4me3, ChIP-seq


title: Bur-0_W+N-_P3ID33_e

value: W+N-


title: Astrocyte day21 rep2


title: Bur-0_W+N-_P3ID33_d


title: K27_RCC2975, H3K27, ChIP-seq

value: Epitehlioid


title: Astrocyte day21 rep1


title: Bur-0_W+N-_P3ID34_c

value: leaf


title: Bur-0_W+N-_P3ID34_b


title: K27_RCC2974, H3K27, ChIP-seq


title: Astrocyte day7 rep2


title: Bur-0_W+N-_P3ID34_a


title: K27_RCC2973, H3K27, ChIP-seq


title: Col-0_W-N+_P3ID33_e


title: Bur-0_W-N+_P3ID33_e


title: Astrocyte day7 rep1


title: Bur-0_W+N-_P3ID33_f


title: Astrocyte day3 rep2


title: Bur-0_W-N+_P3ID33_d


title: Bur-0_W-N+_P3ID33_f


title: K27_RCC2970, H3K27, ChIP-seq


title: Astrocyte day3 rep1


title: Bur-0_W-N+_P3ID34_b


title: K27_RCC2194, H3K27, ChIP-seq


title: K27_RCC2971, H3K27, ChIP-seq


title: Bur-0_W+N+_P3ID33_e


title: Astrocyte day1 rep2


title: K27_RCC2031, H3K27, ChIP-seq


title: Bur-0_W-N+_P3ID34_a


title: Bur-0_W+N+_P3ID33_f


title: Astrocyte day1 rep1


title: Bur-0_W+N+_P3ID33_d


title: K27_RCC1764, H3K27, ChIP-seq


title: mRCCT1258, MeDIP, MeDIP-seq

source_name: Tissue

value: Tissue

value: MeDIP


title: 203271740023_R07C01_Young Adult Cells 10 d_10 d_Young Cells

type: genomic

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using Infinium Methylation NXT setting

data_processing:
Partek Genomic Suite V7 (Using MethylationEPIC_v-1-0_B4 manifest file)
Data is normalised via functional normalisation (with noob background correction)

label: biotin

source_name: DNA from Heterogenous muscle-derived human primary cells (HDMCs)

label_protocol: Labels in title (Beadchip Barcode_Beadchip position_Source_Timepoint_Age condition)

extract_protocol: Genomic DNA was extracted via the Qiagen DNA Easy Kit in accordance with  manufacturers guidelines. The DNA was then bisulfite converted using the EZ DNA Methylation Kit, Zymo Research, CA, United States, as per manufacturer’s instructions.

value: Skeletal Muscle


title: mRCCT1238, MeDIP, MeDIP-seq

value: Sarcomatoid


title: 203271740023_R08C01_Aged Adult Cells 0 h_0 h_Aged Cells


title: 203271740023_R06C01_Young Adult Cells 10 d_10 d_Young Cells


title: Col-0_W-N+_P3ID33_d


title: Bur-0_W-N+_P3ID34_c


title: Astrocyte Sham rep1

value: sham


title: Astrocyte Sham rep2


title: 203271740023_R05C01_Young Adult Cells 7 d_7 d_Young Cells


title: 203271740023_R02C01_Young Adult Cells 72 h_72 h_Young Cells


title: mRCCT1120, MeDIP, MeDIP-seq


title: 203271740023_R03C01_Young Adult Cells 72 h_72 h_Young Cells


title: 203271740023_R04C01_Young Adult Cells 7 d_7 d_Young Cells


title: mRCCT1116, MeDIP, MeDIP-seq


title: AT2 cells, CD44lo_2

data_processing:
Illumina CASAVA was used for base calling
Adapters were trimmed from sequence, and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the reference genome using STAR (Dobin et al, 2013).
Read counts for each gene were calculated using htseq-count (Anders et al, 2015)
Normalization and differntial expression were determined using DESeq2 (Love et al, 2014). Differential expressed genes with FDR-adjusted p-value less than 0.05 were determined significant.
Genome_build: mm10
Supplementary_files_format_and_content: CD44hi_vs CD44lo_Differential_Expression.xlsx: A DESeq2 output containing normalized abundance measurements for each sample.

source_name: Alveolar type 2 cells

extract_protocol:
AT2 cells isolated from SpC-creER/Rosa-mTmG lineage tracing mice were FACS sorted into GFP+CD44hi and GFP+CD44lo populations. Total RNA was extracted using the RNAqueous-Micro Total RNA isolation kit (ThermoFisher). TruSeq mRNA-Seq libraries was prepared and sequenced on the  Illumina Hiseq 4000 platform with production of single-end, 50 bp reads.
The Illiumina Stranded mRNA-Seq library Preparation Kit was used to prepare sequencing libraries.

value: SpC-creER/Rosa-mTmG

value: Lung

value: Alveolar type 2 cells

tag: cell subtype


title: AT2 cells, CD44lo_1


title: 203271740023_R01C01_Young Adult Cells 72 h_72 h_Young Cells


title: 203265020088_R07C01_Young Adult Cells 0 h_0 h_Young Cells


title: AT2 cells, CD44lo_3


title: 203265020088_R06C01_Young Adult Cells 0 h_0 h_Young Cells


title: mRCCT1063, MeDIP, MeDIP-seq


title: 203265020088_R08C01_Young Adult Cells 0 h_0 h_Young Cells


title: 203265020088_R04C01_Young Adult Cells 7 d_7 d_Young Cells


title: mRCCT1072, MeDIP, MeDIP-seq


title: AT2 cells, CD44hi_2


title: mRCCT0826, MeDIP, MeDIP-seq


title: 203265020088_R05C01_Young Adult Cells 7 d_7 d_Young Cells


title: Col-0_W+N+_P3ID34_a

value: W+N+


title: AT2 cells, CD44hi_3


title: 203265020088_R03C01_Young Adult Cells 7 d_7 d_Young Cells


title: AT2 cells, CD44hi_1


title: mRCCT0294, MeDIP, MeDIP-seq


title: 203265020088_R01C01_Young Adult Cells 72 h_72 h_Young Cells


title: 203265020034_R05C01_Aged Adult SkM Tissue_Tissue_Aged Tissue

source_name: DNA from Aged skeletal muscle tissue


title: mRCCT0261, MeDIP, MeDIP-seq


title: LC5 [985]

city: Chengdu

first: xipeng

last: yan

state: Sichuan

address: 26 Huacai Road, Chengdu, China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
The differentially expressed genes (DEGs) were defined at p < 0.05 and fold change > 1.5.
Assembly: GRCh37
Supplementary files format and content: Expression_Gene.xlsx
Supplementary files format and content: Expression_Transcript.xlsx

source_name: PBMC: adult blood

extract_protocol: A total quantity of 1~2 μg total RNA per sample was used and ribosomal RNA (rRNA) was removed using the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, USA). RNA libraries were constructed by KAPA Stranded RNA-Seq Library Prep Kit (KAPA, USA) with pretreated RNAs according to the manufacturer's protocol. After libraries were purified and enriched by PCR, the quality of libraries was controlled by the Agilent 2100 Bioanalyzer (Agilent Technologies Inc, USA). cDNA was denatured as single-stranded DNA and then sequenced for 150 cycles on Illumina HiSeq 4000 (Illumina, USA).

treatment_protocol: patients with HBV related liver cirrhosis (LC),  patients with HBV induced hepatic failure (HF) and  healthy controls (HC)were enrolled in this study, peripheral blood samples collected to abstract PBMC

value: blood

value: PBMC

tag: disease

value: liver cirrhosis


title: LFF5 [979]

value: liver failer combined with fungal infection


title: 203265020034_R04C01_Aged Adult SkM Tissue_Tissue_Aged Tissue


title: 203265000138_R06C01_Aged Adult Cells 10 d_10 d_Aged Cells


title: 203265020034_R01C01_Aged Adult SkM Tissue_Tissue_Aged Tissue


title: mRCCT0244, MeDIP, MeDIP-seq


title: LFF4 [946]


title: LC4 [956]


title: 203265020034_R02C01_Aged Adult SkM Tissue_Tissue_Aged Tissue


title: mRCCT0248, MeDIP, MeDIP-seq


title: 203265000138_R05C01_Aged Adult Cells 10 d_10 d_Aged Cells


title: mRCCT0242, MeDIP, MeDIP-seq


title: 203265000138_R02C01_Aged Adult Cells 7 d_7 d_Aged Cells


title: LF4 [839]

value: liver failure


title: mRCCT0243, MeDIP, MeDIP-seq


title: 203265000138_R04C01_Aged Adult Cells 10 d_10 d_Aged Cells


title: 203265000138_R03C01_Aged Adult Cells 10 d_10 d_Aged Cells


title: 203265000138_R01C01_Aged Adult Cells 7 d _7 d_Aged Cells


title: mRCCT0232, MeDIP, MeDIP-seq


title: 203259760020_R08C01_Aged Adult Cells 7 d _7 d_Aged Cells


title: LFF3 [812]


title: 203265020088_R02C01_Young Adult Cells 7 d_7 d_Young Cells


title: mRCCT0224, MeDIP, MeDIP-seq


title: LFF2 [795]


title: 203259760020_R05C01_Aged Adult Cells 72 h_72 h_Aged Cells


title: 203259760020_R06C01_Aged Adult Cells 72 h_72 h_Aged Cells


title: mRCCT0220, MeDIP, MeDIP-seq


title: 203259760020_R07C01_Aged Adult Cells 72 h_72 h_Aged Cells


title: 203259760020_R04C01_Aged Adult Cells 72 h_72 h_Aged Cells


title: 203265020034_R03C01_Aged Adult SkM Tissue_Tissue_Aged Tissue


title: LF5 [882]


title: 203259760020_R02C01_Aged Adult Cells 0 h_0 h_Aged Cells


title: LF3 [781]


title: LF2 [766]


title: mRCCT0210, MeDIP, MeDIP-seq


title: LF1 [692]


title: mRCCT0164, MeDIP, MeDIP-seq


title: 203259760020_R03C01_Aged Adult Cells 0 h_0 h_Aged Cells


title: 203259750043_R05C01_Young Adult Cells 0 h_0 h_Young Cells


title: mRCCT0156, MeDIP, MeDIP-seq


title: 203259750043_R06C01_Young Adult Cells 72 h_72 h_Young Cells


title: 203259750043_R08C01_Young Adult Cells 72 h_72 h_Young Cells


title: 203259750043_R03C01_Young Adult Cells 0 h_0 h_Young Cells


title: IN_RCCT1306, Input


title: 203259750043_R04C01_Young Adult Cells 0 h_0 h_Young Cells


title: 203259750043_R07C01_Young Adult Cells 72 h_72 h_Young Cells


title: IN_RCCT1120, Input


title: HC4 [1089]

value: healthy control


title: HC3 [1088]


title: HC5 [1090]


title: 203259750043_R02C01_Young Adult Cells 0 h_0 h_Young Cells


title: IN_RCCT1116, Input


title: HC2 [1087]


title: IN_RCCT1072, Input


title: Exp3-TTS(Mono)-R3

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

description: ribosome protected mRNA footprints, approx 26-34 nt

data_processing:
For Exp1, Basecalling was done with RTA version 2.4.11
For Exp2 and Exp3, Basecalling was done using RTA version 2.11.3
Adapter sequence "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" was trimmed using cutadapt 2.1 (HRIBO 1.4.4)
Mapping with segemehl 0.3.4 (HRIBO 1.4.4)
rRNA filtering with samtools 1.9 (HRIBO 1.4.4)
Coverage file creation with HRIBO 1.4.4
wig files were generated with full read or single nucleotide mapping
wig files were normalized using the Counts Per Million (CPM) method and converted to bigwig format
Assembly: ASM908v1
Supplementary files format and content: bigwig format files containing CPM normalized read coverage for each sample
Supplementary files format and content: bigwig format files containing CPM normalized read coverage with specific read-length restrictions for each sample

organism: Campylobacter jejuni

growth_protocol: Bacteria were grown in Brucella broth at 37°C in a microaerobic atmosphere until log phase

extract_protocol:
size-selected RNA from rRNA depleted total RNA or ribosome footprints generated bz micrococcal nuclease
small RNA or adaptor ligation protocol

treatment_protocol: Bacteria were untreated or treated with chloramphenicol, retapamulin, oncocin, or apidaecin 137

value: wild-type

value: apidaecin 137 50 µM


title: Exp3-TIS(Onc)-R3

value: oncocin 50 µM


title: 203259760020_R01C01_Aged Adult Cells 0 h_0 h_Aged Cells


title: Exp3-TTS(Di)-R3

description: ribosome protected mRNA footprints, approx 50-80 nt


title: IN_RCCT1063, Input

value: Tissue


title: LC3 [1072]


title: HC1 [1086]


title: IN_RCCT0826, Input


title: IN_RCCT0164, Input


title: Exp3-TTS(Mono)-R2


title: Exp3-TTS(Di)-R2


title: Exp3-RIBO-R3

value: untreated


title: LC2 [1033]


title: Exp3-TIS(Onc)-R2


title: LFF1 [1047]


title: Exp3-RIBO-R2


title: LC1 [1032]


title: Exp3-TTS(Mono)-R1


title: Exp3-TTS(Di)-R1


title: IN_RCCT0156, Input

value: Sarcomatoid


title: flower of XBAT31 mutant, heat, rep3

city: Hang Zhou

first: 霖霖

last: 张

address: Yuhangtang Road No.866

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: flower

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: flower

value: XBAT31 mutant


title: Exp3-RIBO-R1


title: Exp3-TIS(Onc)-R1


title: flower of XBAT31 mutant, heat, rep2


title: K4_RCCT156, H3K4me2, ChIP-seq


title: Exp3-RNA-R1

description: rRNA depleted total RNA, approx 26-34 nt


title: Exp2-TIS(Ret)-R3

value: delta-cmeB

value: retapamulin 12.5 µg/ml


title: Exp2-RIBO-R3


title: flower of XBAT31 mutant, heat, rep1


title: Exp3-RNA-R3


title: Exp2-RNA-R3


title: flower of XBAT31 mutant, mock, rep3


title: Exp2-TIS(Ret)-R2


title: K4_RCCT1120, H3K4me2, ChIP-seq


title: Exp3-RNA-R2


title: Exp2-RNA-R2


title: Exp2-RIBO-R2


title: K4_RCCT1116, H3K4me2, ChIP-seq


title: flower of XBAT31 mutant, mock, rep2


title: K4_RCCT1072, H3K4me2, ChIP-seq


title: Exp2-RNA-R1


title: K4_RCCT826, H3K4me2, ChIP-seq


title: Exp2-TIS(Ret)-R1


title: K4_RCCT1063, H3K4me2, ChIP-seq


title: Exp1-RNA-R3


title: flower of WT, heat, rep3

value: WT


title: Exp1-RIBO-R3

value: chloramphenicol


title: Exp1-RIBO-R2


title: flower of WT, heat, rep2


title: K4_RCCT0164, H3K4me2, ChIP-seq


title: K27_RCCT1306, H3K27, ChIP-seq


title: Exp1-RNA-R2


title: K4_RCCT1306, H3K4me2, ChIP-seq


title: flower of WT, heat, rep1


title: Exp1-RIBO-R1


title: Exp1-RNA-R1


title: hPMVECs, MMC, 14 hrs, rep3

city: san francisco

first: Akiko

last: Hata

state: CALIFORNIA

address: 555 Mission Bay Blvd. South, CVRI, ucsf, Room 252T

department: Cardiovascular Research Institute

institute: University of California San Francisco

data_processing:
FastQC v0.72  Quality checks
Trimmomatic v0.38.1 to remove low quality reads and any adapter
HISAT2 v2.1.0 for aligment with the GRCh38/hg38 genome
HTSeq-count v0.91  calculate transcript coverage
DESeq2 (v2.11.40) To find differentially expressed transcripts
Supplementary files format and content: Normalized matrix in csv format

source_name: human pulmonary microvascular endothelial cells (hPMVECs)

growth_protocol: hPMVECs were cultured on 0.2% gelatin coated plates in EGM2 growth medium supplemented with EGM2 singleQuots supplement.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). The quality of RNAs was evaluated by 2100 Bioanalyzer Instrument (Agilent Technologies).
Library construction was done by BGI genomics using their inhouse kit.

treatment_protocol: Saline (vehicle) or MMC (150 mM) was added to the culture media (EGM-2 media with supplemented with 0.02% FBS) of hPMVECs at 60-70% confluency and treated for 4h and 14h.

value: MMC

value: 14 hrs


title: K27_RCCT1120, H3K27, ChIP-seq


title: flower of WT, mock, rep3


title: K27_RCCT1116, H3K27, ChIP-seq


title: hPMVECs, MMC, 14 hrs, rep2

value: human pulmonary microvascular endothelial cells (hPMVECs)


title: hPMVECs, MMC, 14 hrs, rep1


title: flower of WT, mock, rep2


title: Exp2-RIBO-R1


title: flower of XBAT31 mutant, mock, rep1


title: hPMVECs, control, 0 hrs, rep3

value: control

value: 0 hrs


title: flower of WT, mock, rep1


title: K27_RCCT1063, H3K27, ChIP-seq


title: hPMVECs, MMC, 4 hrs, rep3

value: 4 hrs


title: hPMVECs, MMC, 4 hrs, rep2


title: hPMVECs, MMC, 4 hrs, rep1


title: hPMVECs, control, 0 hrs, rep2


title: K27_RCCT0826, H3K27, ChIP-seq


title: Saos2, 40 nM Roc, biol replicate 3

city: Columbus

first: Long-Sheng

last: Chang

state: Ohio

address: 575 Children's Crossroad, WC-5574, Ctr for Childhood Cancer & Dept of Pediatrics, Nationwide Children's Hosp & The Ohio State U

department: Center for Childhood Cancer

institute: Research Institute at Nationwide Children's Hospital

data_processing:
Non-polyA-tailed RNA species, including mitochondrial transcripts, rRNAs, and tRNAs, were filtered out using Bowtie 2 (v.2.5.1).
STAR v2.7.3a was used to align reads to the GRCh37/hg19 reference human genome (released February 2009). Raw read counts were estimated via HTSeq v0.11.225 and normalized with the DESeq2 package26. Cufflinks v2.2.1 was used to estimate the gene expression levels27, and the values were reported as FPKM (fragments per kilobase per million) units per gene. DESeq2 was employed to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Raw read counts were estimated via HTSeq v0.11.2 and normalized with the DESeq2 package. Cufflinks v2.2.1 was used to estimate the gene expression levels27, and the values were reported as FPKM (fragments per kilobase per million) units per gene. DESeq2 was employed to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Cufflinks v2.2.1 was used to estimate the gene expression levels, and the values were reported as FPKM (fragments per kilobase per million) units per gene. DESeq2 was employed to estimate the differential expression of gene counts relative to the DMSO-treated controls.
DESeq2 was used to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Assembly: GRCh37/hg19 reference human genome (released February 2009)
Supplementary files format and content: Excel (xlsx) file containing the raw and normalized counts (in FPKM) for all replicates
Supplementary files format and content: Excel (xlsx) file containing the log2-fold change (log2FC) of DDR- and Roc-treated cells compared to DMSO-treated control cells, statstics including P-values and adjusted P-values, and raw and normalized FPKM counts for replicates

growth_protocol: Human osteosarcoma cell lines MG-63 and Saos2 were grown in standard 10-centimeter dishes in high-glucose DMEM with glutamine and 10% heat-inactivated FBS at 37° C in a 5% CO2 humifiied incubator.

extract_protocol:
Maxwell RSC simplyRNA Cells kit (Cat. #AS1390; Promega).
Illumina TruSeq stranded mRNA kit

treatment_protocol: Cells were treated with 0.04% DMSO as a vehicle control or 1x growth-inhibitory IC50 concentration of Roc or DDR for 24 hours. Cells were harvested by scraping down on ice, cell pellets rinsed with cold PBS, and snap-frozen on dry ice

value: osteosarcoma

value: 40 nM Roc

value: 24 hours


title: Saos2, 40 nM Roc, biol replicate 2


title: hPMVECs, control, 0 hrs, rep1


title: ChIP-seq INPUT in Pax6 upregulation ESC

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

institute: IGH, CNRS

data_processing:
Data were mapped using bowtie2, the duplicated reads were discarded and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the methods section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a bigwig file of the two merged replicates.

growth_protocol: ESC were grown in FBS+LIF media with standard conditions. NPCs were differentiated using retinoic acid between days 4 and 8 when the cells were harvested. For detailed protocol see adjoning paper.

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. Cells were lysed and IP done using Diagenone iDeal ChIP-seq kit for TFs or histones according to the manufacturer's recommendation.
Libraries were constructed by BGI

value: mESC upPAX6

value: Pax6 upregulation in mESC


title: ChIP-seq of Pax6 in Pax6 upregulation ESC_R2


title: ChIP-seq of Pax6 in Pax6 upregulation ESC_R1


title: K27_RCCT0164, H3K27, ChIP-seq

value: Tissue

value: Sarcomatoid


title: ChIP-seq INPUT in CTCF motif deletion at element A NPC

source_name: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dCTCF

value: deletion of CTCF motif at element A


title: Saos2, 7 nM DDR, biol replicate 2

value: WT

value: 7 nM DDR


title: K27_RCCT0156, H3K27, ChIP-seq


title: Saos2, 40 nM Roc, biol replicate 1


title: Lactuca sativa, stem, s2, HIT-SOseq, RNAseq

city: Guangzhou

first: Zhuoxing

last: Shi

state: GD

address: #7 Jinsui Road, Tianhe District

department: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: HIT-ISOseq

data_processing:
HIT-ISOseq analysis software kit (https://github.com/shizhuoxing/Lettuce_HIT-ISOseq_Paper) for Full-Length Non-Concatemer (FLNC) reads identification, UMI extraction and correction.
Assembly: Lsat_Salinas_v7
Supplementary files format and content: Tab-separated values files and fasta files

organism: Lactuca sativa

source_name: stem

extract_protocol:
The  amplification procedure refer to HIT-ISOseq.
The  library construction procedures refer to HIT-ISOseq.

value: stem

value: garden lettuce

value: bulk


title: Saos2, 7 nM DDR, biol replicate 1


title: Lactuca sativa, stem, s1, HIT-SOseq, RNAseq

description: HIT-ISOseq


title: K27_RCCT1072, H3K27, ChIP-seq


title: ChIP-seq of Pol2 in CTCF motif deletion at element A NPC_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: Saos2, DMSO, biol replicate 1

value: DMSO


title: Lactuca sativa, leaf, s2, HIT-SOseq, RNAseq

description: HIT-ISOseq

source_name: leaf

value: leaf


title: Saos2, DMSO, biol replicate 2

value: osteosarcoma


title: ChIP-seq of Rad21 in CTCF motif deletion at element A NPC_R2


title: MG-63, 25 nM Roc, replicate 2

value: 25 nM Roc


title: MG-63, 5 nM DDR, biol replicate 2

value: 5 nM DDR

value: 24 hours


title: Lactuca sativa, leaf, s1, HIT-SOseq, RNAseq

description: HIT-ISOseq


title: Lactuca sativa, root, s2, HIT-SOseq, RNAseq

description: HIT-ISOseq

source_name: root

value: root


title: MG-63, 5 nM DDR, biol replicate 1


title: ChIP-seq of CTCF in CTCF motif deletion at element A NPC_R2


title: Saos2, 7 nM DDR, biol replicate 3


title: MG-63, DMSO, biol replicate 1


title: Lactuca sativa, root, s1, HIT-SOseq, RNAseq

description: HIT-SOseq


title: PC3,HSR, WGS

city: Stanford

first: Guiping

address: 256 Campus Dr

institute: Stanford University

description: WGS

data_processing:
We   utilized   AmpliconSuite-pipeline   (v1.2.2,   https://github.com/AmpliconSuite/AmpliconSuite- pipeline)   which   invoked   CNVKit  (v0.9.9),  AmpliconArchitect  (v1.3.r8)   and  AmpliconClassifier (v1.1.2).   In   brief,   the   analysis   pipeline   first   identifies   seed   regions   of   focal   amplification   from whole   genome   copy   number   calls,   then   among   the   seed   regions   AmpliconArchitect   (AA) analyzes   copy   number   and   structural   variation   jointly   to   construct   a   local   genome   graph encoding   structural   rearrangements   and   copy   numbers.  AA  then   extracts   genome   paths   and cycles   from   the   genome   graph   which   explain   the   observed   changes   in   copy   number   and structural variation. The outputs of AA are passed to AmpliconClassifier (AC), which applies a rule-based method to match the patterns of copy number, structural variation, and structures extracted from the genome graph to known types of focal amplifications, such as ecDNA. To minimize   sequencing   artifacts   derived   from   insert   size   distribution   variance,   we   set   the AmpliconSuite-pipeline argument --AA_insert_sdevs 9. For PC3 samples, --downsample 1 was also set to reduce additional sequencing artifacts. Default parameters were used otherwise
Assembly: hg38
Supplementary files format and content: URL
Supplementary files format and content: https://ampliconrepository.org/project/6639560c48cbf4a5ccffad4d

source_name: Prostate Cancer

growth_protocol: PC3-DM and PC3-HSR cells are maintained in  4.5 g/L glucose formulated Dulbecco’s Modified Eagle’s Medium (Corning, #10-013-CV) supplemented with 10% FBS and 1% Penicillin-Streptomycin-Glutamine. The cells are maintained as adherent culture at 37C with 5% CO2.

extract_protocol:
gDNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer's protocol.
WGS library was prepared using 250ng gDNA with FS DNA Library Prep Kit from NEB, following manufacturer's protocol.

value: Prostate Cancer

value: Epithelial


title: ChIP-seq of CTCF in CTCF motif deletion at element A NPC_R1

value: NPC dCTCF


title: PC3, DM, WGS

description: WGS


title: ChIP-seq of Pol2 in CTCF motif deletion at element A NPC_R2

value: deletion of CTCF motif at element A


title: Saos2, DMSO, biol replicate 3

value: WT


title: ChIP-seq of H3K27Ac in CTCF motif deletion at element A NPC_R2


title: ros1_salt_G7

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
For data analysis, low base quality reads were trimmed using Trimmomatic with parameter "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". The remaining high quality sequences were mapped to Arabidopsis reference genome using BSMAP.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bigWig files give methylation level for Cs  with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

source_name: seedlings

growth_protocol: Plants were grown on soil under long day conditions (23 °C, 16h light, 8h dark)

extract_protocol:
Three-week-old seedlings were collected for genomic DNA extraction using DNeasy Plant Maxi Kit (Qiagen, 68163)
Genomic DNA was processed at the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China). Libraries were prepared for bisulfite sequencing according to the manufacturer’s (Illumina) instructions and were sequenced on an Illumina HiSeq 2500 platform.

tag: ecotype

tag: genotype/variation

tag: generation

tag: agent

value: salt


title: ros1_G7


title: MG-63, 25 nM Roc, biol replicate 1

tag: cell line

tag: cell type

tag: treatment


title: Col-0_G7

value: wildtype


title: ChIP-seq INPUT in CTCF motif deletion at element A ESC

value: mESC dCTCF

tag: genotype


title: sample3

city: Luzhou

first: Xiaomei

last: Xu

state: None Selected

address: China

institute: Southwest medical univercity

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such a the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler R package（3.8.1） to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Assembly: GRCh36
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: periodontal ligament

extract_protocol:
Total RNA was extracted by Trizol from the cells of various treatment groups.
Library preparation for Transcriptome sequencing

tag: tissue

value: periodontal ligament

value: periodontal ligament stem cells

value: Homo sapiens

value: control


title: sample5

value: Naringenin treated


title: sample6


title: sample8


title: sample4


title: sample7


title: ChIP-seq of Rad21 in CTCF motif deletion at element A NPC_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: MG-63, DMSO, biol replicate 2

value: osteosarcoma

value: DMSO


title: sample2


title: sample1


title: control fibroblasts, S3

city: Shanghai

first: Xia

last: Fang

address: No. 639 Zhizaoju Road

institute: Shanghai 9th People’s Hospital

data_processing:
Stringtie software is first used to count the fragments within each gene locus after alignment, followed by normalization using the TMM (trimmed mean of M values) algorithm, and finally, calculating the FPKM value for each gene.
For the sequences aligned to specific genes in the genome obtained from sequencing, statistical quantification is performed using the edgeR software. This involves calculating the number of sequencing reads corresponding to each gene and normalizing them across samples. This process constitutes gene quantification calculation. Based on the experimental grouping information, differential genes between two groups are then calculated.
Assembly: GRCh38.100
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

source_name: control fibroblasts

extract_protocol:
RNA was harvested using Tianmo#TR205-200 kit. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SureSelect Strand-Specific RNA Component kit following manufacturer's protocols.

value: control fibroblasts


title: ros1_salt_G10_rep5


title: ChIP-seq of Pol2 in CTCF motif deletion at element A ESC_R2


title: ChIP-seq of Pol2 in CTCF motif deletion at element A ESC_R1


title: control fibroblasts, S1


title: onychofibroblasts, N3

source_name: onychofibroblasts

value: onychofibroblasts


title: ros1_salt_G10_rep2


title: ros1_salt_G10_rep4


title: control fibroblasts, S2


title: ChIP-seq of H3K27Ac in CTCF motif deletion at element A NPC_R1


title: onychofibroblasts, N2


title: ChIP-seq of Rad21 in CTCF motif deletion at element A ESC_R1


title: onychofibroblasts, N1


title: PBMC_29 [VU951]

city: Amsterdam

first: Yongsoo

last: Kim

address: De Boelelaan 1118

country: Netherlands

institute: University Medical Center Amsterdam, Location VUmc

data_processing:
The following pipeline was used to create featurecounts.txt from raw sequence reads: https://github.com/tgac-vumc/RNA-seq/tree/master
Assembly: Homo_sapiens.GRCh37.75.dna.primary_assembly
Supplementary files format and content: Text file containing RNA counts for each sample

source_name: blood

extract_protocol:
RNA was isolated using the Invitrogen (Thermo Fisher Scientific) protocol according to manufacturer’s instructions
Libraries were prepared using the KAPA mRNA HyperPrep Kit according to manufacturer's instructions

value: blood

value: PBMC

tag: disease state

value: Glioblastoma


title: ChIP-seq of CTCF in CTCF motif deletion at element A ESC_R2

value: deletion of CTCF motif at element A


title: PBMC_32 [VU909]

value: Meningioma


title: PBMC_31 [VU938]


title: ChIP-seq of CTCF in CTCF motif deletion at element A ESC_R1


title: PBMC_18 [VU924]

value: Astrocytoma


title: nrpd1_salt_G10_rep4

value: salt


title: PBMC_27 [VU944]


title: PBMC_39 [VU906]


title: nrpd1_salt_G10_rep3


title: ChIP-seq of H3K27Ac in CTCF motif deletion at element A ESC_R1

value: mESC dCTCF


title: PBMC_1 [VU903]


title: ChIP-seq of H3K27Ac in CTCF motif deletion at element A ESC_R2


title: ros1_salt_G10_rep3


title: PBMC_23 [VU897]


title: PBMC_4 [VU886]


title: nrpd1_salt_G10_rep2


title: nrpd1_salt_G10_rep1


title: ChIP-seq of Rad21 in CTCF motif deletion at element A ESC_R2


title: PBMC_6 [VU877]


title: PBMC_16 [VU871]


title: ChIP-seq INPUT in element AB deletion NPC

value: NPC dAB

value: double deletion of elements A and B


title: Col-0_salt_G10_rep5

value: wildtype


title: ChIP-seq of Pax6 in element AB deletion NPC_R1


title: Col-0_salt_G10_rep4


title: PBMC_34 [VU858]


title: PBMC_19 [VU866]


title: ros1_salt_G10_rep1


title: Col-0_salt_G10_rep3


title: PBMC_5 [VU856]


title: ChIP-seq of Pol2 in element AB deletion NPC_R1


title: PBMC_17 [VU838]


title: PBMC_30 [VU847]


title: PBMC_37 [VU833]


title: Col-0_salt_G10_rep2


title: Col-0_salt_G10_rep1


title: ChIP-seq of Pol2 in element AB deletion NPC_R2


title: PBMC_33 [VU815]


title: ChIP-seq of Pax6 in element AB deletion NPC_R2


title: PBMC_15 [VU819]


title: ChIP-seq of Rad21 in element AB deletion NPC_R2


title: ros1_G10_rep5


title: ChIP-seq of CTCF in element AB deletion NPC_R2


title: PBMC_35 [VU872]


title: ros1_G10_rep4


title: PBMC_36 [VU798]


title: ChIP-seq of CTCF in element AB deletion NPC_R1


title: PBMC_25 [VU799]


title: ros1_G10_rep3


title: ChIP-seq of H3K36me3 in element AB deletion NPC_R2


title: ros1_G10_rep2


title: PBMC_3 [VU779]


title: PBMC_0 [VU776]


title: PBMC_22 [VU766]


title: ros1_G10_rep1


title: ChIP-seq of H3K36me3 in element AB deletion NPC_R1


title: PBMC_13 [VU731]


title: PBMC_47 [VU810]


title: PBMC_20 [VU831]


title: PBMC_12 [VU756]


title: ChIP-seq of H3K27Ac in element AB deletion NPC_R2


title: ChIP-seq of Rad21 in element AB deletion NPC_R1


title: nrpd1_G10_rep4


title: nrpd1_G10_rep5


title: PBMC_40 [VU807]


title: PBMC_14 [VU710]


title: PBMC_38 [VU697]


title: PBMC_24 [VU702]


title: PBMC_46 [VU729]


title: ChIP-seq of H3K27Ac in element AB deletion NPC_R1


title: PBMC_8 [VU700]


title: PBMC_43 [VU690]


title: ChIP-seq of H3K4me3 in element AB deletion NPC_R2


title: nrpd1_G10_rep2


title: PBMC_9 [VU662]


title: nrpd1_G10_rep1


title: PBMC_41 [VU647]


title: ChIP-seq INPUT in element AB deletion ESC

value: mESC dAB


title: PBMC_44 [VU668]


title: ChIP-seq of H3K4me3 in element AB deletion NPC_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: PBMC_26 [VU661]


title: Col-0_G10_rep5


title: PBMC_11 [VU637]


title: ChIP-seq of Pol2 in element AB deletion ESC_R2


title: ChIP-seq of Pol2 in element AB deletion ESC_R1


title: PBMC_45 [HD107]

value: Healthy


title: Col-0_G10_rep4


title: PBMC_10 [HD106]


title: nrpd1_G10_rep3


title: PBMC_7 [VU474]


title: Col-0_G10_rep3


title: ChIP-seq of Rad21 in element AB deletion ESC_R2


title: PBMC_42 [HD105]


title: PBMC_21 [HD127]


title: Young9

first: Sijia

last: Li

state: Beijing

address: No. 1 Dahua Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequencing on the Illumina NovaSeq 6000 system was followed by an image analysis, base calling, and quality control to generate the raw reads. Quality control was initially performed using the Q30 threshold. Adapters and low-quality reads were removed using the Cutadapt software program (version 1.9.3), resulting in high-quality reads. These reads were then aligned to the reference genome using the Bismark software program (version 0.16.3). The Bismark Methylation Extractor component was used to determine the genome-wide methylation status of each cytosine (C) site. EM-seq facilitates the examination of C methylation at a single-base resolution. We used the methylation_extractor command in Bismark to quantify the methylation of each C across the entire genome. The outcomes were presented in a bedGraph format file, along with a coverage file that included counts for each C site.
Assembly: Assembly: hg19
Supplementary files format and content: For the processed data file named "Bismark_Methylated_rate.tsv" . Format: Tab-Separated Values (TSV). Content: Contains methylation percentage data. The first column lists chromosomes, the second column specifies the position of cytosine (C) on the chromosome, and subsequent columns represent the methylation rate for each sample, expressed as a percentage.

source_name: Plasma

extract_protocol:
cfDNA was extracted from 2-3 ml of plasma samples using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Quantification of genomic DNA was carried out using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, USA). The prepared library was then sequenced on an Illumina NovaSeq 6000 system (Illumina) in 150-bp paired-end sequencing mode.
The extracted cfDNA was then subjected to adapter ligation using a NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs, Ipswich, MA, USA) [19]. Post-ligation, 5-methylcytosine and 5-hydroxymethylcytosine in cfDNA were oxidized using TET enzymes, preventing them from undergoing deamination by subsequent APOBEC enzymes. Conversely, unmodified cytosines are deaminated by APOBEC enzymes, converting them into uracil. Subsequently, the enzymatically converted cfDNA was subjected to polymerase chain reaction (PCR) amplification and purification to obtain the final EM-Seq library.

value: Plasma

tag: Sex

value: Female

value: untreated


title: ChIP-seq of CTCF in element AB deletion ESC_R1


title: Young7


title: ros1_G1


title: PBMC_2 [HD078]

value: blood


title: Young5

value: Male


title: nrpd1_G1


title: PBMC_28 [HD063]

value: PBMC


title: Col-0_G1


title: Col-0_G10_rep2


title: Col-0_G10_rep1


title: ChIP-seq of CTCF in element AB deletion ESC_R2


title: Young8


title: ChIP-seq of Rad21 in element AB deletion ESC_R1


title: sEV_LPS_3

first: Long-Xin

last: Huang

address: No. 58, Zhongshan 2nd Road

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
Data analysis is based on R language version 4.2.0
Perform differential expression analysis using DeSeq2 package and enrichment analysis (GO and KEGG) using clusterProfile package
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone

growth_protocol: As described previously, for BMDCs, 3×106 bone marrow cells per well were cultured in 6 well plates in 3 mL complete medium (RPMI 1640 supplemented with 10% Fetal Bovine Serum (FBS), glutamine, penicillin, 2-mercaptoethanol, streptomycin and HEPES buffer) (ThermoFisher) added with 20 ng/mL GM-CSF and 5 ng/mL IL-4 (Peprotech)

extract_protocol:
Total RNA was extracted from BMDCs using RNAiso Plus reagent (Takara, Japan) according to the manufactures’ protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone

value: Primary

value: Mouse bone marrow-derived DCs

value: WT

value: sEV+LPS


title: Young10


title: sEV_LPS_2


title: ChIP-seq of H3K27Ac in element AB deletion ESC_R2


title: Young4


title: Young6


title: sEV_LPS_1


title: Young11


title: Young2


title: ChIP-seq of H3K27Ac in element AB deletion ESC_R1


title: Young1


title: ChIP-seq of H3K36me3 in element AB deletion ESC_R1


title: Old9


title: sEV_3

value: sEV


title: Young3


title: Old8


title: ChIP-seq of H3K4me3 in element AB deletion ESC_R2

value: double deletion of elements A and B


title: Old4


title: Old6


title: ChIP-seq of H3K36me3 in element AB deletion ESC_R2


title: Old7


title: ChIP-seq of H3K4me3 in element AB deletion ESC_R1


title: ChIP-seq of Pax6 in element B deletion NPC_R2

value: NPC dB

value: deletion of element B


title: Old5


title: Old14


title: Old13


title: Old12


title: sEV_2


title: ChIP-seq INPUT in element B deletion NPC

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: Old3


title: sEV_1


title: Old1


title: Middle-age9


title: PBS_LPS_3

value: PBS+LPS


title: Old2

value: Plasma


title: Middle-age7

value: Female


title: Middle-age8

value: untreated


title: ChIP-seq of Rad21 in element B deletion NPC_R2


title: ChIP-seq of Pax6 in element B deletion NPC_R1


title: Old11


title: Middle-age5


title: ChIP-seq of Rad21 in element B deletion NPC_R1


title: PBS_LPS_1


title: Old10


title: ChIP-seq of CTCF in element B deletion NPC_R2


title: ChIP-seq of Pol2 in element B deletion NPC_R1


title: PBS3

value: PBS


title: PBS_LPS_2


title: Middle-age6


title: PBS2


title: bone_O-Ctrl1-CR-15_tech_rep3

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition

data_processing:
FastQC (v 0.11.8) and MultiQC (v 1.6) were used to check the quality metrics of the datasets. Reads containing adapter sequences were filtered out using Trim Galore (v 0.5.0). Filtered reads were mapped to the mm10 reference genome using the alignment tools STAR (v 2.6.1). FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were quantified with StringTie (v 2.1.3b) and count matrix was generated in R (v 4.1.1). Expression values for each gene were averaged from 4 sequencing technical replicates.
Assembly: mm10
Supplementary files format and content: Comma-separated value files

source_name: bone, old, ctrl

extract_protocol:
Tibia bones were isolated by completely removing adherent muscle and connective tissue, and were immediately frozen in liquid nitrogen and stored at -80°C until further processing. RNA was extracted from whole-tissue, ground to a powder while frozen in liquid nitrogen, using the phenol/chloroform method. Specifically, an aliquot of approximately 50 mg of tissue powder was vortexed for one minute with 200 µl of Trizol (Thermo Fisher Scientific). After centrifugation at 12,000g for 10 minutes at 4°C, supernatant was transferred to a new tube and 40µl of chloroform were added. Samples were centrifuged for 15 minutes at 12,000g and 4°C, followed by RNA precipitation from the collected upper clear phase with 250 μl of isopropanol. RNA was purified by washing in 500 μl of 75% ethanol, dried and solubilized in 30 μl DEPC-treated, i.e. RNAse-free, water. DNase digest of purified RNA was performed using the Invitrogen Turbo DNA-free kit (Thermo Fisher Scientific). An Agilent 2100 BioAnalyzer (Agilent RNA 6000 Nano Kit) was used to check for total RNA quality of the samples.
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina), with a selected insert size of 120–210 bp, and sequenced on an Illumina HiSeq 4000 instrument.

value: whole bone

tag: age

value: old

value: ctrl


title: Middle-age4

value: Male


title: Middle-age3


title: bone_O-Ctrl1-CR-15_tech_rep4


title: Middle-age1


title: ChIP-seq of H3K36me3 in element B deletion NPC_R2


title: bone_O-Ctrl1-CR-15_tech_rep2


title: Middle-age10


title: iMAC_Spn14_rep2

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

data_processing:
Illumina Casava software was used for basecalling.
Reads were trimmed with the Trim Galore (v0.6.7) software with the these parameters: "--nextera --fastqc --paired --clip_R1 15 --clip_R2 15 --three_prime_clip_R1 5 --three_prime_clip_R2 5 --length 30". Then adaptor-trimmed paired-end RNA-seq reads were mapped to GRCh38 human genome using STAR (v2.7.10b) with default parameters. The STAR output read counts for each sample were combined. Subsequent differential expression analysis were done using R package DESeq2(V1.40.1).
Assembly: GRCh38
Supplementary files format and content: Text files of gene names and read counts for each sample.

source_name: cultured cells

growth_protocol: H1 cells were maintained on Growth Factor Reduced Matrigel-coated well plates in TeSR-E8 medium.

extract_protocol:
Total RNA was extracted using TRIzol acrroding to the instruction mannual.
RNA-seq library was prepared following the Smart-seq2 protocol (Picelli, 2014)

treatment_protocol: For monolayer based macrophage differentiation, pluripotent stem cells were first cultured in E8 medium, after replating, E8 medium was changed to RPMI1640 medium with AATS supplement without insulin, supplemented with BMP4 in the first day and with BMP4 and CHIR99021 in the following 2 days. After 3 days of induction, cells were replated and cultured in RPMI1640 medium with RPMI1640 mainly supplemented with B27 supplement, VEGF, and bFGF. After 2-day induction, SB431542 was added. After another 3 days of induction, floating CD34+CD43+ cells were collected as HSPCs. The HSPCs were further induced in RPMI1640 mainly supplemented with B27 supplement, M-CSF, and IL-3 for 6 days, and all cells were collected and cultured in RPMI1640 with FBS and M-CSF added for more than 2 days. And the mature iMACs were obtained as the adherent cells in the culture. Then  iMACs were subjected to the stimulation of S. pneumoniae serotype 14.

value: cultured cells

value: human embryonic stem cell line H1-derived macrophage-like cells

tag: passage number

value: stimulated by S. pneumoniae serotype 14


title: Middle-age2


title: ChIP-seq of H3K36me3 in element B deletion NPC_R1


title: ChIP-seq of Pol2 in element B deletion NPC_R2


title: iMAC_Spn14_rep1


title: iMAC_rep1

value: control


title: COLO320, HSR, H3K36me3, rep2

description: H3K36me3 ChIP-seq

data_processing:
The sequence data were trimmed by Trimmomatic22 (v0.36) to remove adapter
Reads were mapped to the hg38 assembly of the human genome using Bowtie2 with the following settings: --local --very-sensitive --phred33 -X 1000.
Reads with MAPQ values less than 10 were filtered using SAMtools (v1.8)
Duplicate reads were removed using picard-tools.
Bigwig (.bw) files were generated for each strand using bamCoverage (py-deeptools/3.3.1_py36) with -binSize 10 --normalizeUsing CPM
Input normalized bigwig (.bw) files were generated using bamCompare default settings.
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files contain normalized DNA signals  for visualization.
Supplementary files format and content: Bigwig (.bw) files (normalized_log2Ratio) contain CHIP signals normalized to input for visualization.

growth_protocol: RPMI, 10% FBS, 1% pen/strep

extract_protocol:
Cells were fixed in 1% formaldehyde for 15min with rotation then quenched with 0.125M glycine. After cell membrane lysis and then nuclear lysis, chromatin was sonicated using a Vocariss E220 sonicator (140W, 10% duty, 200 cycles/burst, 600sec/sample).
NEBNext Ultra II DNA library prep kit with NEBNext multiplex oligos; 6 cycles of amplification

tag: chip antibody

value: H3K36me3 abcam ab9053

value: colorectal carcinoma


title: bone_O-CR-7_tech_rep4

source_name: bone, old, calorie restriction

value: calorie restriction


title: iMAC_rep2


title: PBS1

value: bone

value: Primary

value: Mouse bone marrow-derived DCs

value: WT


title: ChIP-seq of H3K27Ac in element B deletion NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dB

value: deletion of element B


title: ChIP-seq of CTCF in element B deletion NPC_R1


title: COLO320, DM, H3K36me3, rep2

description: H3K36me3 ChIP-seq

value: H3K36me3 abcam ab9051


title: bone_O-CR-7_tech_rep3

value: whole bone

value: old


title: COLO320, DM, H3K36me3, rep1

description: H3K36me3 ChIP-seq

value: H3K36me3 abcam ab9050


title: ChIP-seq of H3K27Ac in element B deletion NPC_R1


title: ChIP-seq of H3K4me3 in element B deletion NPC_R2


title: COLO320, HSR, input, rep2

description: ChIP-seq input


title: COLO320, DM, input, rep2

description: ChIP-seq input


title: bone_O-Ctrl1-CR-15_tech_rep1

value: ctrl


title: ChIP-seq of H3K4me3 in element B deletion NPC_R1


title: COLO320, HSR, input, rep1

description: ChIP-seq input


title: bone_O-CR-7_tech_rep1